Variant report

Variant	rs2403023
Chromosome Location	chr12:83358930-83358931
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10746259	0.88[GIH][hapmap];0.81[JPT][hapmap]
rs10746261	0.88[GIH][hapmap];0.81[JPT][hapmap]
rs10778923	0.81[GIH][hapmap];0.80[MEX][hapmap]
rs10862525	0.84[ASN][1000 genomes]
rs10862526	0.92[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs10862527	0.82[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.81[MKK][hapmap];0.93[ASN][1000 genomes]
rs10862528	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10862529	1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs10862530	1.00[ASW][hapmap];0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10862531	0.88[YRI][hapmap]
rs10862532	0.90[ASN][1000 genomes]
rs12297736	0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs12320912	0.85[ASN][1000 genomes]
rs12809082	0.87[JPT][hapmap]
rs1471781	0.86[ASN][1000 genomes]
rs1625397	0.97[ASN][1000 genomes]
rs1682590	0.97[ASN][1000 genomes]
rs1682592	0.99[ASN][1000 genomes]
rs1682593	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs1682594	0.99[ASN][1000 genomes]
rs1682595	0.97[ASN][1000 genomes]
rs17010268	0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs1796188	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1796189	0.99[ASN][1000 genomes]
rs2019384	0.81[GIH][hapmap];0.87[JPT][hapmap]
rs2403020	0.92[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs2403021	0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3993374	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4346030	0.85[ASN][1000 genomes]
rs4346031	0.97[ASN][1000 genomes]
rs7295699	0.97[ASN][1000 genomes]
rs7957916	0.92[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs7965229	0.82[ASN][1000 genomes]
rs7970086	0.92[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7971263	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521849	chr12:83013783-83991479	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv469490	chr12:83089431-83507269	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv559542	chr12:83089431-83507269	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv832472	chr12:83248283-83419753	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
5	nsv559557	chr12:83334204-83453620	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
6	nsv469495	chr12:83339933-83374779	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
7	nsv559558	chr12:83339933-83374779	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:83347000-83367200	Weak transcription	Gastric	stomach
2	chr12:83347000-83379600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:83349400-83374600	Weak transcription	Colon Smooth Muscle	Colon
4	chr12:83356200-83379400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr12:83356400-83381600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr12:83356600-83359200	Enhancers	Brain Hippocampus Middle	brain
7	chr12:83356600-83381400	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr12:83357800-83359000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr12:83357800-83363200	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr12:83357800-83389600	Weak transcription	Fetal Intestine Large	intestine
11	chr12:83358000-83359200	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr12:83358000-83389600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr12:83358200-83366200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr12:83358200-83368400	Weak transcription	Fetal Stomach	stomach
15	chr12:83358400-83359200	Weak transcription	Fetal Lung	lung
16	chr12:83358400-83361600	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr12:83358400-83363000	Weak transcription	Fetal Brain Male	brain
18	chr12:83358400-83366400	Weak transcription	Brain Substantia Nigra	brain
19	chr12:83358400-83397600	Weak transcription	Brain Anterior Caudate	brain
20	chr12:83358400-83409200	Weak transcription	Brain Angular Gyrus	brain
21	chr12:83358600-83359000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:83358600-83359400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:83358600-83362200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr12:83358600-83368400	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr12:83358600-83372200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr12:83358600-83379400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr12:83358600-83394200	Weak transcription	Fetal Muscle Leg	muscle
28	chr12:83358600-83399600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr12:83358600-83409400	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr12:83358800-83359600	Weak transcription	Stomach Smooth Muscle	stomach
31	chr12:83358800-83362800	Weak transcription	Brain Germinal Matrix	brain

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